Variant report

Variant	rs12080668
Chromosome Location	chr1:151167921-151167922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr1:151167725-151168030	ECC-1	luminal epithelium:	n/a	n/a
2	TEAD4	chr1:151167680-151168261	ECC-1	luminal epithelium:	n/a	n/a
3	BCL3	chr1:151167554-151168147	A549	lung:	n/a	n/a
4	JUND	chr1:151167601-151168291	MCF-7	breast:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167953-151167964 chr1:151167956-151167967 chr1:151167954-151167965
5	SP1	chr1:151167500-151168284	HCT-116	colon:	n/a	chr1:151167983-151167993
6	RCOR1	chr1:151167042-151168530	Hela-S3	cervix:	n/a	n/a
7	REST	chr1:151167669-151168108	MCF-7	breast:	n/a	n/a
8	CREB1	chr1:151167701-151168172	A549	lung:	n/a	chr1:151167898-151167911
9	ZKSCAN1	chr1:151167701-151168076	Hela-S3	cervix:	n/a	n/a
10	EGR1	chr1:151167853-151168051	K562	blood:	n/a	chr1:151168005-151168020 chr1:151167977-151167992 chr1:151167986-151167999
11	TEAD4	chr1:151167674-151168197	HCT-116	colon:	n/a	n/a
12	BCL3	chr1:151167644-151168213	A549	lung:	n/a	n/a
13	POLR2A	chr1:151167506-151167930	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr1:151166739-151169180	Hela-S3	cervix:	n/a	n/a
15	GABPA	chr1:151167664-151168052	A549	lung:	n/a	n/a
16	JUND	chr1:151167574-151168223	T-47D	breast:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167953-151167964 chr1:151167956-151167967 chr1:151167954-151167965
17	MAX	chr1:151167688-151168110	Hela-S3	cervix:	n/a	chr1:151167845-151167854
18	FOXA1	chr1:151167660-151167998	T-47D	breast:	n/a	n/a
19	TCF7L2	chr1:151167725-151167940	MCF-7	breast:	n/a	n/a
20	FOXA2	chr1:151167716-151168076	A549	lung:	n/a	n/a
21	JUND	chr1:151167674-151168130	Hela-S3	cervix:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167953-151167964 chr1:151167956-151167967 chr1:151167954-151167965
22	JUND	chr1:151167511-151168270	HCT-116	colon:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167953-151167964 chr1:151167956-151167967 chr1:151167954-151167965
23	MAX	chr1:151167606-151168386	MCF-7	breast:	n/a	chr1:151167845-151167854
24	NR3C1	chr1:151167711-151168043	A549	lung:	n/a	n/a
25	JUND	chr1:151167574-151168208	A549	lung:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167953-151167964 chr1:151167956-151167967 chr1:151167954-151167965
26	TAF1	chr1:151167700-151168051	Hela-S3	cervix:	n/a	n/a
27	GTF2F1	chr1:151167725-151168064	Hela-S3	cervix:	n/a	n/a
28	HDAC2	chr1:151167777-151168095	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:151167227-151168056	U87	brain:	n/a	n/a
30	STAT3	chr1:151167732-151168069	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr1:151167407-151168117	U87	brain:	n/a	n/a
32	MAX	chr1:151167672-151168182	A549	lung:	n/a	chr1:151167845-151167854
33	CEBPB	chr1:151167628-151168187	MCF-7	breast:	n/a	n/a
34	E2F4	chr1:151167683-151167984	MCF10A-Er-Src	breast:	n/a	n/a
35	FOXA1	chr1:151167700-151168014	T-47D	breast:	n/a	n/a
36	MYC	chr1:151167691-151168064	MCF10A-Er-Src	breast:	n/a	chr1:151167845-151167854
37	EGR1	chr1:151167590-151168276	MCF-7	breast:	n/a	chr1:151168005-151168020 chr1:151167977-151167992 chr1:151167986-151167999
38	POLR2A	chr1:151167781-151167959	HepG2	liver:	n/a	n/a
39	JUND	chr1:151167588-151168222	A549	lung:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167953-151167964 chr1:151167956-151167967 chr1:151167954-151167965
40	CEBPB	chr1:151167663-151168209	HCT-116	colon:	n/a	n/a
41	CTCF	chr1:151167900-151168050	RPTEC	kidney:	n/a	n/a
42	MAX	chr1:151167481-151168269	MCF-7	breast:	n/a	chr1:151167845-151167854
43	CTCF	chr1:151167840-151167990	HEEpiC	esophagus:	n/a	n/a
44	EGR1	chr1:151167557-151168441	HCT-116	colon:	n/a	chr1:151168005-151168020 chr1:151167977-151167992 chr1:151167986-151167999
45	STAT3	chr1:151167690-151168028	Hela-S3	cervix:	n/a	n/a
46	JUND	chr1:151167026-151168270	HCT-116	colon:	n/a	chr1:151167955-151167963 chr1:151167955-151167963 chr1:151167955-151167962 chr1:151167953-151167964 chr1:151167956-151167967 chr1:151167954-151167965
47	GATA3	chr1:151167566-151168280	MCF-7	breast:	n/a	n/a
48	EP300	chr1:151167511-151168285	A549	lung:	n/a	chr1:151167955-151167964
49	MYC	chr1:151167855-151168007	MCF-7	breast:	n/a	n/a
50	YY1	chr1:151167675-151168011	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151162057..151164706-chr1:151165181..151172008,8	K562	blood:
2	chr1:151167521..151168494-chr3:149530058..149530684,2	Hela-S3	cervix:
3	chr1:151166423..151168363-chr1:151318010..151319809,2	MCF-7	breast:
4	chr1:151167814..151170369-chr1:151245194..151246986,2	MCF-7	breast:
5	chr1:151165541..151174157-chr1:151252015..151257857,16	MCF-7	breast:
6	chr1:151156826..151164982-chr1:151165389..151172985,25	MCF-7	breast:
7	chr1:151166432..151169145-chr1:151169439..151172527,5	MCF-7	breast:
8	chr1:151166438..151169666-chr1:151298490..151301352,3	MCF-7	breast:
9	chr1:151164944..151168688-chr1:151252728..151255250,4	MCF-7	breast:
10	chr1:151041779..151043840-chr1:151166772..151169795,3	MCF-7	breast:
11	chr1:151167452..151169662-chr1:151226503..151228827,3	MCF-7	breast:

Variant related genes	Relation type
PIP5K1A	TF binding region
VPS72	TF binding region
ENSG00000143458	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000082996	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143390	Chromatin interaction
ENSG00000273481	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000237976	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11204788	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11204789	1.00[AMR][1000 genomes]
rs11204790	1.00[AMR][1000 genomes]
rs11204797	1.00[AMR][1000 genomes]
rs11204799	1.00[AMR][1000 genomes]
rs11204800	1.00[AMR][1000 genomes]
rs11204801	1.00[AMR][1000 genomes]
rs11204802	1.00[AMR][1000 genomes]
rs11204804	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12057875	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12058806	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12065050	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12068012	0.82[AFR][1000 genomes]
rs12071605	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12073695	1.00[AMR][1000 genomes]
rs12077026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077958	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12082248	1.00[AMR][1000 genomes]
rs12086389	1.00[AMR][1000 genomes]
rs12087802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089598	0.82[AFR][1000 genomes]
rs12090291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12090912	0.82[AFR][1000 genomes]
rs12092749	1.00[AMR][1000 genomes]
rs12094954	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61751621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6661777	1.00[AMR][1000 genomes]
rs9887870	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151162800-151170200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:151162800-151170400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:151163000-151170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:151163200-151168600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:151163200-151168600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:151163200-151170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:151163200-151170400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:151163200-151170400	Weak transcription	Gastric	stomach
9	chr1:151163200-151170400	Weak transcription	Left Ventricle	heart
10	chr1:151163400-151168200	Weak transcription	GM12878-XiMat	blood
11	chr1:151163400-151168600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:151163400-151168600	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:151163400-151168600	Weak transcription	Psoas Muscle	Psoas
14	chr1:151163400-151168800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:151163400-151168800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:151163400-151169000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:151163400-151170000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:151163400-151170200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:151163400-151170200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:151163400-151170200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:151163400-151170200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:151163400-151170200	Weak transcription	Brain Substantia Nigra	brain
23	chr1:151163400-151170400	Weak transcription	Primary T cells from cord blood	blood
24	chr1:151163600-151168800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:151163600-151170200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:151163600-151170200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:151163600-151170200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:151163800-151168600	Weak transcription	Dnd41	blood
29	chr1:151163800-151168800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:151163800-151169000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:151163800-151169000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:151166400-151168000	Enhancers	HMEC	breast
33	chr1:151166400-151168200	Enhancers	NHLF	lung
34	chr1:151166400-151169200	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr1:151166600-151168600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:151166600-151169200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:151166800-151170200	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr1:151167000-151169200	Active TSS	Duodenum Mucosa	Duodenum
39	chr1:151167000-151169600	Active TSS	Placenta	Placenta
40	chr1:151167000-151172000	Active TSS	Colonic Mucosa	Colon
41	chr1:151167200-151168200	Active TSS	NHEK	skin
42	chr1:151167200-151168600	Weak transcription	Stomach Mucosa	stomach
43	chr1:151167200-151168800	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr1:151167200-151168800	Active TSS	Hela-S3	cervix
45	chr1:151167200-151169800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:151167400-151169000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:151167400-151169200	Active TSS	A549	lung
48	chr1:151167400-151169600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:151167600-151168000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:151167600-151168200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links